I made about a gallon of salsa last week. We ate a bunch, and I froze a little bit, but I didn't peel the tomatoes, and have my doubts about how satisfactory the frozen stuff will be.
So this morning when I cleaned out my fridge, I realized today was the 6th day for the stuff, and it was either pitch or use immediately. I put the salsa in the nuke and cooked it uncovered until it was all thickened and bubbly, about 20 minutes at 5 minute intervals. Then I ran it through the food mill, and came up with some good thick & spicy sauce to add to my chili next winter.

I've done a similar thing too - I've poured my leftover home made salsa over chicken breasts and baked it @ 350 till juices run clear. It's quite tasty, and the jalepeno mellows out just enough. When serving, I top it with slices of avocado and a bit of shredded jack cheese.